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Metallic surface dynamics of genomic DNA and its nitrogenous bases: SERS assessment and theoretical considerations

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Abstract

The dynamics of genomic DNA and its nucleobases at a silver surface were explored using surface-enhanced Raman spectroscopy (SERS) and ab initio Verlet-type dynamics, respectively. The bands observed had full widths at half-maximum (FWHMs) in the wavenumber range 10–29 cm−1. (Sub)picosecond molecular dynamics with global relaxation times of 0.37–1.06 ps were noted. Furthermore, the on-surface ab initio dynamics of the DNA bases were examined using DFT with a Verlet-type algorithm. The results attained for these ergodic dynamic systems describe real systems quite well and could therefore be correlated with corresponding experimental data.

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References

  1. Hinz JM, Rodriguez Y, Smerdon MJ (2010) Rotational dynamics of DNA on the nucleosome surface markedly impact accessibility to a DNA repair enzyme. Proc Natl Acad Sci USA 107:4646–4651

    Article  CAS  Google Scholar 

  2. Arugula MA, Yang F, Somasundaram S, Easley C, Shannon C, Simonian AL (2015) Surface dynamics study of DNA loop formation using surface plasmon resonance. ECS Trans 66:19–29

    Article  CAS  Google Scholar 

  3. Zidovska A (2017) The “self-stirred” genome: bulk and surface dynamics of the chromatin globule. Biophys J 112(3):180a

    Article  Google Scholar 

  4. Hüsken N, Gębala M, La Mantia F, Schuhmann W, Metzler-Nolte N (2011) Mechanistic studies of fc-PNA (•DNA) surface dynamics based on the kinetics of electron-transfer processes. Chem Eur J 17:9678–9690

    Article  Google Scholar 

  5. Chang C-M, Lau Y-G, Ou S-C, Lin T-Y, Juan W-T (2015) Anomalous diffusion of DNA on a supported cationic lipid membrane. EPL 109(3):38002

    Article  Google Scholar 

  6. Schmitt TJ, Rogers JB, Knotts IV TA (2013) Exploring the mechanisms of DNA hybridization on a surface. J Chem Phys 138(3):035102

    Article  PubMed  Google Scholar 

  7. Hogg T, Zhang M, Yang R (2008) Modeling and analysis of DNA hybridization dynamics at microarray surface in moving fluid. In: IEEE (ed) IEEE International Conference on Robotics and Automation, Pasadena, CA, USA. IEEE, Piscataway, pp 3419–3424

  8. Kholmurodov KT, Dushanov EB, Krasavin EA, Hassan HK, ElHabashy HA, Galal A, Sweilam NH, Yasuoka K (2013) Molecular dynamics simulations of the DNA interaction with metallic nanoparticles and TiO2 surfaces. In: Kholmurodov KT (ed) Models in bioscience and materials research. Nova Science, Hauppauge, pp 167–200

  9. Izanloo C (2017) Effect of gold nanoparticle on stability of the DNA molecule: a study of molecular dynamics simulation. Nucleosides Nucleotides Nucleic Acids 36:571–582

    CAS  PubMed  Google Scholar 

  10. Maleki A, Alavi S, Najafi B (2011) Molecular dynamics simulation study of adsorption and patterning of DNA bases on the Au(111) surface. J Phys Chem C 115:22484–22494

    Article  CAS  Google Scholar 

  11. Pipolo S, Corni S (2016) Real-time description of the electronic dynamics for a molecule close to a plasmonic nanoparticle. J Phys Chem C 120:28774–28781

    Article  CAS  Google Scholar 

  12. Muntean CM, Bratu I, Leopold N, Morari C, Buimaga-Iarinca L, Purcaru MAP (2015) Subpicosecond surface dynamics in genomic DNA from in vitro-grown plant species: a SERS assessment. Phys Chem Chem Phys 17:21323–21330

    Article  CAS  PubMed  Google Scholar 

  13. Muntean CM, Bratu I, Leopold N (2011) Molecular relaxation processes in genomic DNA from leaf tissues: a surface-enhanced Raman spectroscopic study. Spectroscopy 26:245–254

    Article  CAS  Google Scholar 

  14. Muntean CM, Bratu I, Leopold N, Purcaru MAP (2011) Subpicosecond dynamics in DNA from leaves of in vitro-grown apple plants: a SERS study. Spectroscopy 26:59–68

    Article  CAS  Google Scholar 

  15. Muntean CM, Leopold N, Tripon C, Coste A, Halmagyi A (2015) Surface-enhanced Raman spectroscopy of genomic DNA from in vitro grown tomato (Lycopersicon esculentum Mill.) cultivars before and after plant cryopreservation. Spectrochim Acta A 144:107–114

    Article  CAS  Google Scholar 

  16. Muntean CM, Bratu I, Hernanz A (2017) Vibrational relaxation of the backbone and base modes in LacDNA complexes by UV resonance Raman spectroscopy. J Phys Chem B 121:6909–6918

    Article  CAS  PubMed  Google Scholar 

  17. Soler JM, Artacho E, Gale JD, García A, Junquera J, Ordejón P, Sánchez-Portal D (2002) The SIESTA method for ab initio order-N materials simulation. J Phys Condens Matter 14:2745–2779

  18. Ordejón P, Artacho E, Soler JM (1996) Self-consistent order-N density functional calculations for very large systems. Phys Rev B 53:R10441–R10444

    Article  Google Scholar 

  19. Verlet L (1967) Computer “experiments” on classical fluids. I. Thermodynamical properties of Lennard-Jones molecules. Phys Rev 159:98–103

    Article  CAS  Google Scholar 

  20. Wang CZ, Fasolino A, Tosatti E (1988) Molecular-dynamics theory of the temperature-dependent surface phonons of W(001). Phys Rev B 37:2116–2122

    Article  CAS  Google Scholar 

  21. Muntean CM, Bratu I, Bogdan D (2013) Subpicosecond processes in nucleic acids bases monitored by Raman spectroscopy. Biomed Spectrosc Imaging 2:37–49

  22. Santamaria R, Charro E, Zacarías A, Castro M (1999) Vibrational spectra of nucleic acid bases and their Watson–Crick pair complexes. J Comput Chem 20:511–530

  23. Calborean A, Buimaga-Iarinca L (2012) DFT simulation of vibrational properties of adenine adsorbed on gold surface: the effect of periodic boundary conditions. Comput Theor Chem 993:106–112

    Article  CAS  Google Scholar 

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Acknowledgements

The authors wish to thank Prof. Dr. Nicolae Leopold (Babeş-Bolyai University, Cluj-Napoca, Romania) for the surface-enhanced Raman spectroscopic measurements, Dr. Ana Coste and Dr. Adela Halmagyi (National Institute of Research and Development for Biological Sciences, Branch Institute of Biological Research, Cluj-Napoca, Romania) for extracting genomic DNA from tomato leaves, and two of our colleagues: Dr. Cristian Morari for useful discussions on theoretical considerations and Dr. Carmen Tripon for help with data processing. This work was partially supported by a grant from the Ministry of National Education, National Authority for Scientific Research, National Council of Scientific Research-Unit Executive for Funding Higher Education, Research, Development and Innovation (CNCS-UEFISCDI), Romania (project number PN-II-ID-PCE-2012-4-0115).

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  1. National Institute for Research & Development of Isotopic and Molecular Technologies, 67-103 Donat St., RO-400293, Cluj-Napoca, Romania

    Cristina M. Muntean, Teodor-Lucian Biter, Ioan Bratu & Nicoleta Toşa

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  1. Cristina M. Muntean
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  2. Teodor-Lucian Biter
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  3. Ioan Bratu
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  4. Nicoleta Toşa
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Correspondence to Cristina M. Muntean.

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Muntean, C.M., Biter, TL., Bratu, I. et al. Metallic surface dynamics of genomic DNA and its nitrogenous bases: SERS assessment and theoretical considerations. J Mol Model 25, 162 (2019). https://doi.org/10.1007/s00894-019-4039-y

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  • DOI: https://doi.org/10.1007/s00894-019-4039-y

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